# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 10:41:46 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(1~{R},2~{S},3~{R},5~{S},6~{R})-2-(hydroxymethyl)-3,5,6-tris(oxidanyl)cyclohexyl]oxy-oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)C[C@@H](O)[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 5QP  5QP  (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(1~{R},2~{S},3~{R},5~{S},6~{R})-2-(hydroxymethyl)-3,5,6-tris(oxidanyl)cyclohexyl]oxy-oxane-3,4,5-triol  D-saccharide  47  23  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5QP
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 5QP  O2    O  OH1   0  -0.695   1.3895  -2.8992  -0.4548
 5QP  C2    C  CH1   0   0.001   1.9861  -1.6475  -0.6638
 5QP  C3    C  CH1   0  -0.012   2.7848  -1.1789   0.5513
 5QP  O3    O  OH1   0  -0.677   3.8106  -2.0883   0.8796
 5QP  C4    C  CH1   0   0.035   3.4427   0.1616   0.2467
 5QP  O4    O  OH1   0  -0.674   4.0826   0.7034   1.3763
 5QP  C5    C  CH1   0  -0.023   2.3808   1.1596  -0.2141
 5QP  C6    C  CH2   0  -0.155   2.9942   2.4671  -0.6670
 5QP  O6    O  OH1   0  -0.669   1.9620   3.3464  -1.0728
 5QP  O5    O  O2    0  -0.499   1.6625   0.6305  -1.3175
 5QP  C1    C  CH1   0   0.212   0.9829  -0.5648  -1.0682
 5QP  O1    O  O2    0  -0.515   0.0457  -0.4222  -0.0448
 5QP  CAX   C  CH1   0   0.022  -1.3383  -0.3571  -0.3384
 5QP  CAT   C  CH1   0   0.049  -2.0014  -1.5092   0.4082
 5QP  OAI   O  OH1   0  -0.679  -1.4413  -2.7106  -0.0762
 5QP  CAO   C  CH1   0   0.027  -3.5102  -1.4839   0.2244
 5QP  OAD   O  OH1   0  -0.678  -4.0279  -2.5820   0.9460
 5QP  CAN   C  CH2   0  -0.519  -4.0584  -0.1547   0.7162
 5QP  CAR   C  CH1   0   0.054  -3.4259   1.0104  -0.0336
 5QP  OAG   O  OH1   0  -0.670  -3.8794   2.2486   0.4703
 5QP  CAV   C  CH1   0  -0.281  -1.9017   1.0052   0.0816
 5QP  CAK   C  CH2   0  -0.167  -1.2757   2.1616  -0.7234
 5QP  OAB   O  OH1   0  -0.711  -0.5917   3.0680   0.1132
 5QP  H21   H  HOH1  0   0.451   0.4894  -2.7837  -0.1078
 5QP  H22   H  HCH1  0   0.230   2.6858  -1.7627  -1.5009
 5QP  H31   H  HCH1  0   0.212   2.1023  -1.0439   1.4035
 5QP  H32   H  HOH1  0   0.454   3.4016  -2.9067   1.1787
 5QP  H41   H  HCH1  0   0.210   4.1590   0.0119  -0.5780
 5QP  H42   H  HOH1  0   0.455   4.7380   0.0678   1.6822
 5QP  H51   H  HCH1  0   0.232   1.6988   1.3603   0.6228
 5QP  H62   H  HCH2  0   0.227   3.5681   2.8877   0.1625
 5QP  H61   H  HCH2  0   0.206   3.6928   2.2790  -1.4921
 5QP  H63   H  HOH1  0   0.470   2.3157   4.2403  -1.1065
 5QP  H11   H  HCH1  0   0.253   0.4943  -0.8329  -2.0127
 5QP  HAX1  H  HCH1  0   0.233  -1.5001  -0.4986  -1.4176
 5QP  HAT1  H  HCH1  0   0.216  -1.7859  -1.3895   1.4822
 5QP  HAI1  H  HOH1  0   0.461  -1.8560  -3.4463   0.3882
 5QP  HAO1  H  HCH1  0   0.213  -3.7308  -1.5931  -0.8483
 5QP  HAD1  H  HOH1  0   0.457  -4.9415  -2.7221   0.6795
 5QP  HAN1  H  HCH2  0   0.248  -5.1452  -0.1311   0.5839
 5QP  H1    H  HCH2  0   0.232  -3.8593  -0.0497   1.7881
 5QP  HAR1  H  HCH1  0   0.203  -3.6861   0.9165  -1.1006
 5QP  HAG1  H  HOH1  0   0.450  -4.8238   2.3149   0.2986
 5QP  HAV1  H  HCH1  0   0.242  -1.6493   1.1532   1.1390
 5QP  HAK1  H  HCH2  0   0.213  -0.6054   1.7639  -1.4895
 5QP  HAK2  H  HCH2  0   0.203  -2.0677   2.6873  -1.2696
 5QP  HAB1  H  HOH1  0   0.454   0.2915   3.2166  -0.2564

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 5QP  CAN  CAO   single  1.520  0.020  1.520
 5QP  CAN  CAR   single  1.523  0.020  1.523
 5QP  OAG  CAR   single  1.412  0.020  1.412
 5QP  OAD  CAO   single  1.412  0.020  1.412
 5QP  CAO  CAT   single  1.520  0.020  1.520
 5QP  CAR  CAV   single  1.529  0.020  1.529
 5QP  CAV  CAX   single  1.533  0.020  1.533
 5QP  CAV  CAK   single  1.542  0.020  1.542
 5QP  CAT  OAI   single  1.411  0.020  1.411
 5QP  CAT  CAX   single  1.525  0.020  1.525
 5QP  OAB  CAK   single  1.410  0.020  1.410
 5QP  CAX  O1    single  1.416  0.020  1.416
 5QP  O1   C1    single  1.395  0.020  1.395
 5QP  O5   C1    single  1.397  0.020  1.397
 5QP  O5   C5    single  1.419  0.020  1.419
 5QP  C1   C2    single  1.530  0.020  1.530
 5QP  C6   C5    single  1.514  0.020  1.514
 5QP  C6   O6    single  1.415  0.020  1.415
 5QP  C5   C4    single  1.528  0.020  1.528
 5QP  C2   O2    single  1.402  0.020  1.402
 5QP  C2   C3    single  1.528  0.020  1.528
 5QP  C4   C3    single  1.524  0.020  1.524
 5QP  C4   O4    single  1.407  0.020  1.407
 5QP  C3   O3    single  1.410  0.020  1.410
 5QP  O2   H21   single  0.850  0.020  0.980
 5QP  C2   H22   single  0.970  0.020  1.090
 5QP  C3   H31   single  0.970  0.020  1.090
 5QP  O3   H32   single  0.850  0.020  0.980
 5QP  C4   H41   single  0.970  0.020  1.090
 5QP  O4   H42   single  0.850  0.020  0.980
 5QP  C5   H51   single  0.970  0.020  1.090
 5QP  C6   H62   single  0.970  0.020  1.090
 5QP  C6   H61   single  0.970  0.020  1.090
 5QP  O6   H63   single  0.850  0.020  0.980
 5QP  C1   H11   single  0.970  0.020  1.090
 5QP  CAX  HAX1  single  0.970  0.020  1.090
 5QP  CAT  HAT1  single  0.970  0.020  1.090
 5QP  OAI  HAI1  single  0.850  0.020  0.980
 5QP  CAO  HAO1  single  0.970  0.020  1.090
 5QP  OAD  HAD1  single  0.850  0.020  0.980
 5QP  CAN  HAN1  single  0.970  0.020  1.090
 5QP  CAN  H1    single  0.970  0.020  1.090
 5QP  CAR  HAR1  single  0.970  0.020  1.090
 5QP  OAG  HAG1  single  0.850  0.020  0.980
 5QP  CAV  HAV1  single  0.970  0.020  1.090
 5QP  CAK  HAK1  single  0.970  0.020  1.090
 5QP  CAK  HAK2  single  0.970  0.020  1.090
 5QP  OAB  HAB1  single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 5QP  H21   O2   C2    109.95  3.000
 5QP  H22   C2   C1    106.90  3.000
 5QP  H22   C2   C3    107.80  3.000
 5QP  C1    C2   C3    109.62  3.000
 5QP  H22   C2   O2    106.94  3.000
 5QP  C3    C2   O2    112.19  3.000
 5QP  C1    C2   O2    113.08  3.000
 5QP  H31   C3   C4    108.34  3.000
 5QP  H31   C3   O3    110.50  3.000
 5QP  C4    C3   O3    107.45  3.000
 5QP  H31   C3   C2    109.24  3.000
 5QP  O3    C3   C2    111.58  3.000
 5QP  C4    C3   C2    109.67  3.000
 5QP  H32   O3   C3    108.17  3.000
 5QP  H41   C4   C5    108.33  3.000
 5QP  H41   C4   O4    110.94  3.000
 5QP  C5    C4   O4    107.86  3.000
 5QP  H41   C4   C3    108.09  3.000
 5QP  O4    C4   C3    112.01  3.000
 5QP  C5    C4   C3    109.55  3.000
 5QP  H42   O4   C4    108.09  3.000
 5QP  H51   C5   O5    110.27  3.000
 5QP  H51   C5   C6    108.78  3.000
 5QP  O5    C5   C6    107.14  3.000
 5QP  H51   C5   C4    108.72  3.000
 5QP  C6    C5   C4    111.88  3.000
 5QP  O5    C5   C4    110.04  3.000
 5QP  H61   C6   H62   107.60  3.000
 5QP  H61   C6   O6    110.81  3.000
 5QP  H62   C6   O6    111.19  3.000
 5QP  H61   C6   C5    109.56  3.000
 5QP  H62   C6   C5    108.55  3.000
 5QP  O6    C6   C5    109.08  3.000
 5QP  H63   O6   C6    108.61  3.000
 5QP  C1    O5   C5    115.24  3.000
 5QP  H11   C1   O1    110.95  3.000
 5QP  H11   C1   O5    105.80  3.000
 5QP  O1    C1   O5    111.73  3.000
 5QP  H11   C1   C2    110.28  3.000
 5QP  O5    C1   C2    109.48  3.000
 5QP  O1    C1   C2    108.59  3.000
 5QP  CAX   O1   C1    120.60  3.000
 5QP  HAX1  CAX  CAV   109.20  3.000
 5QP  HAX1  CAX  CAT   108.62  3.000
 5QP  CAV   CAX  CAT   112.18  3.000
 5QP  HAX1  CAX  O1    109.94  3.000
 5QP  CAT   CAX  O1    106.78  3.000
 5QP  CAV   CAX  O1    110.07  3.000
 5QP  HAT1  CAT  CAO   108.07  3.000
 5QP  HAT1  CAT  OAI   110.45  3.000
 5QP  CAO   CAT  OAI   111.50  3.000
 5QP  HAT1  CAT  CAX   108.07  3.000
 5QP  OAI   CAT  CAX   107.62  3.000
 5QP  CAO   CAT  CAX   111.09  3.000
 5QP  HAI1  OAI  CAT   108.28  3.000
 5QP  HAO1  CAO  CAN   109.26  3.000
 5QP  HAO1  CAO  OAD   110.33  3.000
 5QP  CAN   CAO  OAD   112.49  3.000
 5QP  HAO1  CAO  CAT   108.37  3.000
 5QP  OAD   CAO  CAT   106.81  3.000
 5QP  CAN   CAO  CAT   109.48  3.000
 5QP  HAD1  OAD  CAO   108.65  3.000
 5QP  H1    CAN  HAN1  107.25  3.000
 5QP  H1    CAN  CAR   109.45  3.000
 5QP  HAN1  CAN  CAR   109.65  3.000
 5QP  H1    CAN  CAO   109.57  3.000
 5QP  HAN1  CAN  CAO   109.74  3.000
 5QP  CAR   CAN  CAO   111.10  3.000
 5QP  HAR1  CAR  CAV   107.94  3.000
 5QP  HAR1  CAR  OAG   110.15  3.000
 5QP  CAV   CAR  OAG   107.24  3.000
 5QP  HAR1  CAR  CAN   108.26  3.000
 5QP  CAV   CAR  CAN   111.99  3.000
 5QP  OAG   CAR  CAN   111.21  3.000
 5QP  HAG1  OAG  CAR   108.19  3.000
 5QP  HAV1  CAV  CAK   107.98  3.000
 5QP  HAV1  CAV  CAR   107.55  3.000
 5QP  CAK   CAV  CAR   111.28  3.000
 5QP  HAV1  CAV  CAX   107.42  3.000
 5QP  CAK   CAV  CAX   111.98  3.000
 5QP  CAR   CAV  CAX   110.42  3.000
 5QP  HAK2  CAK  HAK1  105.57  3.000
 5QP  HAK2  CAK  OAB   109.73  3.000
 5QP  HAK1  CAK  OAB   110.62  3.000
 5QP  HAK2  CAK  CAV   109.05  3.000
 5QP  HAK1  CAK  CAV   110.01  3.000
 5QP  OAB   CAK  CAV   111.66  3.000
 5QP  HAB1  OAB  CAK   108.32  3.000

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 5QP  chir_01  C2   C1   O2   C3   positiv
 5QP  chir_02  C3   O3   C2   C4   positiv
 5QP  chir_03  C4   O4   C3   C5   negativ
 5QP  chir_04  C5   O5   C4   C6   negativ
 5QP  chir_05  C1   O1   O5   C2   negativ
 5QP  chir_06  CAX  O1   CAV  CAT  positiv
 5QP  chir_07  CAT  OAI  CAX  CAO  negativ
 5QP  chir_08  CAO  OAD  CAT  CAN  positiv
 5QP  chir_09  CAR  OAG  CAN  CAV  positiv
 5QP  chir_10  CAV  CAR  CAX  CAK  negativ

